nf-core_modules/software/gatk4/splitncigarreads/meta.yml

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name: gatk4_splitncigarreads
description: Splits reads that contain Ns in their cigar string
keywords:
- vcf
- merge
tools:
- gatk4:
description: |
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
with a primary focus on variant discovery and genotyping. Its powerful processing engine
and high-performance computing features make it capable of taking on projects of any size.
homepage: https://gatk.broadinstitute.org/hc/en-us
documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s
doi: 10.1158/1538-7445.AM2017-3590
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test']
- bam:
type: list
description: BAM/SAM/CRAM file containing reads
pattern: "*.{bam,sam,cram}"
- fasta:
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type: tuple of files
description: |
Tuple of fasta file (first), sequence dict (second) and fasta index (third)
pattern: ["*.fasta", "*.dict", "*.fai"]
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output:
- bam:
type: file
description: Output file with split reads (BAM/SAM/CRAM)
pattern: "*.{bam,sam,cram}"
- version:
type: file
description: File containing software version
pattern: "*.version.txt"
authors:
- "@kevinmenden"